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Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
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SYSNO ASEP 0558580 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search Author(s) Vaňková Hausnerová, Viola (MBU-M) ORCID
Marvalová, Olga (MBU-M)
Šiková, Michaela (MBU-M) ORCID
Shoman, Mahmoud (MBU-M)
Havelková, Jarmila (MBU-M)
Kambová, Milada (MBU-M)
Janoušková, Martina (MBU-M) RID, ORCID
Kumar, Dilip (MBU-M) ORCID
Halada, Petr (MBU-M) RID, ORCID
Schwarz, Marek (MBU-M) ORCID, RID
Krásný, Libor (MBU-M) RID, ORCID
Hnilicová, Jarmila (MBU-M) RID, ORCID
Pánek, Josef (MBU-M) RIDArticle number 848536 Source Title Frontiers in Microbiology. - : Frontiers Research Foundation - ISSN 1664-302X
Roč. 13, MAY 11 2022 (2022)Number of pages 18 s. Language eng - English Country CH - Switzerland Keywords 6s rna ; escherichia-coli ; sp-nov. ; short transcripts ; noncoding rnas ; glycomyces ; release ; growth ; sequence ; requires ; sRNA ; Actinobacteria ; Ms1 RNA ; Streptomyces ; gene synteny ; Mycobacterium ; 6s rna Subject RIV EE - Microbiology, Virology OECD category Microbiology R&D Projects GA20-07473S GA ČR - Czech Science Foundation (CSF) GA20-12109S GA ČR - Czech Science Foundation (CSF) LM2018131 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) ED1.1.00/02.0109 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Open access Institutional support MBU-M - RVO:61388971 UT WOS 000804003100001 EID SCOPUS 85130934622 DOI 10.3389/fmicb.2022.848536 Annotation Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes. Workplace Institute of Microbiology Contact Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Year of Publishing 2023 Electronic address https://www.frontiersin.org/articles/10.3389/fmicb.2022.848536/full
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